This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. It has been suggested that chromatin-involved epigenetic mechanisms affect the accessibility of effector proteins and regulate important downstream cellular activities via modifications of chromatin structure resulting from combinatorial covalent modifications of histones. Despite its significance, comprehensive characterization of modifications on human histone H3 remains a challenge for both traditional peptide-based and recently developed intact protein based mass spectrometry because of the overwhelming number of modifications on it. We will tackle the problem by developing a top-down mass spectrometry method combining the power of Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR MS) with Electron Capture Dissociation (ECD) and that of bioinformatics. This method should be able to analyze the extremely complicated modifications of human Histone H3 and to enable deciphering the relationship between the structure of histone and its biological functions.